SSR data for maize landraces from Central Italy

SSR data for maize landraces from Central Ital

Linkage Disequilibrium and Genome-Wide Association Mapping in Tetraploid Wheat (<i>Triticum turgidum</i> L.)

<div><p>Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (<i>Triticum turgidum</i> ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker–trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker–trait associations.</p></div

Expert-comptable rédacteur d'acte : défaut d'un conseil éclairé aux cédants de parts sociales et préjudice

<p>Asterisks (*) indicate DArT markers putatively under selection.</p

Overview of LD in the intrachromosomal pairs for the whole collection, the <i>durum</i> sub-sample, and the Q1 and Q2 groups, and for genomes A and B.

<p>Mean allele frequency correlations (<i>r²</i>) for all pairs, number (N°) of pairs and percentage (%) significant in LD (<i>P</i><0.01), N° and % of physically linked pairs (<i>r²</i>>critical <i>r²</i>), N° of pairs in complete LD (<i>r²</i> = 1).</p

Evidence for Introduction Bottleneck and Extensive Inter-Gene Pool (Mesoamerica x Andes) Hybridization in the European Common Bean (<i>Phaseolus vulgaris</i> L.) Germplasm

<div><p>Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (<i>Phaseolus vulgaris</i> L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and <i>Pv-shatterproof1</i>) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from “pure” accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and <i>Pv-shatterproof1</i> markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with “pure” accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.</p> </div

Representative markers significantly associated with the thousand kernel weight trait, for the whole collection (normal), the <i>durum</i> sub-sample (underlined), and both (<b>bold</b>).

<p>Asterisks (*) indicate DArT markers putatively under selection.</p

Overview of the LD parameter <i>r²</i>of the intrachromosomal pairs in the whole collection (Pop) (a), in the <i>durum</i> sub-sample (b), and in the two Q groups, Q1 (c) and Q2 (d).

<p>The scatterplots show the distributions of the LD parameter <i>r²</i> according to the genetic distance. The horizontal line indicates the 95% percentile of the distribution of the unlinked <i>r²</i>, which gives the critical value of <i>r²</i>.</p

Number of accessions for each subspecies included in the whole wheat collection and in the Q1 and Q2 subgroups.

<p>Number of accessions for each subspecies included in the whole wheat collection and in the Q1 and Q2 subgroups.</p

DArT markers coverage, distribution, index of diversity and loss of diversity among the whole collection and <i>durum</i> sub-sample, with the distribution and index of diversity in the two Q groups identified in the whole collection.

<p>DArT markers coverage, distribution, index of diversity and loss of diversity among the whole collection and <i>durum</i> sub-sample, with the distribution and index of diversity in the two Q groups identified in the whole collection.</p

Comparison of the two models for the calculation of the associations between the mapped and unmapped markers, and the traits, for the whole collection and the <i>durum</i> sub-sample.

<p>GLM  =  general linear model (Q matrix), MLM  =  mixed linear model (Q matrix + kinship matrix), sign.  =  significant with <i>P</i><0.05.</p